Started by an SCM change000082926819940.997793779519071977917791597c47faf30cea562966e64eedc259a5074c6cf89b1c47faf30cea562966e64eedc259a5074c6cf89b1refs/remotes/origin/masterc47faf30cea562966e64eedc259a5074c6cf89b1c47faf30cea562966e64eedc259a5074c6cf89b1refs/remotes/origin/masterc47faf30cea562966e64eedc259a5074c6cf89b1c47faf30cea562966e64eedc259a5074c6cf89b1refs/remotes/origin/masterhttps://github.com/larson-group/clubb.githttp://carson.math.uwm.edu/jenkins/job/clubb_BFB_r8029_flags_gfortran_test/lastSuccessfulBuild/artifacthttp://carson.math.uwm.edu/jenkins/job/clubb_BFB_r8029_flags_gfortran_test/changeshttp://carson.math.uwm.edu/jenkins/job/clubb_BFB_r8029_flags_gfortran_test/lastSuccessfulBuild/pipeline-overviewhttp://carson.math.uwm.edu/jenkins/job/clubb_BFB_r8029_flags_gfortran_test/lastSuccessfulBuild/testReportfalseUpdate sys_admin RepoRun Python Testfalse#5978292693290clubb_BFB_r8029_flags_gfortran_test #597597false59710762SUCCESS1792225629044http://carson.math.uwm.edu/jenkins/job/clubb_BFB_r8029_flags_gfortran_test/597/- .agents/skills/clubb-doc-language/SKILL.md.agents/skills/clubb-file-descriptions/SKILL.md.agents/skills/clubb-documentation/SKILL.mdAGENTS.md.agents/skills/clubb-change-messages/SKILL.md.agents/skills/clubb-readmes/SKILL.md.agents/skills/clubb-code-comments/SKILL.mdc179bae7435e6e90a0f796cb621d9de4690429b81792177736000http://carson.math.uwm.edu/jenkins/user/noreplynoreplynoreply@github.comAdd CLUBB documentation skills (#1397)
* Add CLUBB documentation skills
Add focused guidance for READMEs, file descriptions, routine/code comments,
and plain language, with a documentation entry skill selected by AGENTS.md.
This gives agents one route to the writing rules for the current task.
Shorten the existing PR/commit guide and require BFB discussion only when a
change could plausibly affect model results or scientific output.
All 18 skill definitions and 45 local guidance links validate; git diff
--check passes.
* Require code reading and checks before finishing documentation
Route small documentation edits through the writing skills. Require agents
to inspect the implementation before drafting and check facts, coverage,
links, and comment syntax before finishing. Clarify that weak file headers
need complete descriptions in the appropriate language form.
Validation: all 18 skill schemas, 46 local guidance links, and whitespace
checks pass. The fresh-agent study uses these exact frozen guidance files.
* Clarify documentation wording and optional usage examples
Explain meaning before usage and make important ordering clear. Read the
applicable language or porting standards for documentation conventions.
Describe file interfaces independently of current callers, using callers as
optional examples. Recommend examples in file headers when useful, or beside
individual routines for collections of independent helpers.
Validation: all 18 skill schemas, 49 local guidance links, and whitespace
checks pass. These refinements have not had a new fresh-agent trial.
2026-10-16 14:08:56 -0500c179bae7435e6e90a0f796cb621d9de4690429b8Add CLUBB documentation skills (#1397)edit.agents/skills/clubb-change-messages/SKILL.mdadd.agents/skills/clubb-code-comments/SKILL.mdadd.agents/skills/clubb-readmes/SKILL.mdadd.agents/skills/clubb-doc-language/SKILL.mdadd.agents/skills/clubb-file-descriptions/SKILL.mdeditAGENTS.mdadd.agents/skills/clubb-documentation/SKILL.md
- .agents/skills/clubb-column-refactor/SKILL.mdjenkins_tests/README.md.agents/skills/clubb-jenkins/test-authoring/SKILL.md.agents/skills/clubb-jenkins/SKILL.md.agents/skills/clubb-documentation/code-comments/SKILL.md.agents/skills/clubb-testing-and-reporting/SKILL.md.agents/skills/clubb-documentation/file-descriptions/SKILL.md.agents/skills/clubb-script-cli/SKILL.md.agents/skills/clubb-fortran-port/SKILL.md.agents/skills/clubb-python-api/SKILL.md.agents/skills/clubb-documentation/readmes/SKILL.md.agents/skills/clubb-numerical-diagnosis/SKILL.md.agents/skills/clubb-documentation/language/SKILL.md.agents/skills/clubb-readmes/SKILL.md.agents/skills/clubb-code-comments/SKILL.mdjenkins_tests/jenkins_api_login.py.agents/skills/clubb-jax-port/SKILL.md.agents/skills/clubb-doc-language/SKILL.md.agents/skills/clubb-file-descriptions/SKILL.md.agents/skills/clubb-documentation/SKILL.md.agents/skills/clubb-host-compatibility/SKILL.md.agents/skills/clubb-finalization/SKILL.mdAGENTS.md.agents/skills/clubb-documentation/change-messages/SKILL.md.agents/skills/clubb-pytests/SKILL.md.agents/skills/clubb-change-messages/SKILL.mdeb23a4c1b51706cad0060c28d8c5ead8da595e1c1792199605000http://carson.math.uwm.edu/jenkins/user/noreplynoreplynoreply@github.comAdd Jenkins workflows and branch finalization guidance (#1396)
* Set up Jenkins API login over HTTPS
Add an interactive token login script and teach the Jenkins skill to reuse
its private local credential file or direct users through setup. This lets
each developer use their own Jenkins account without SSH access.
Ten focused regression checks and a live HTTPS login/save check passed.
BFB is not applicable: login tooling and guidance do not affect model
execution or output.
* Explain Jenkins login setup and agent use
Describe why agents use the saved login, how developers set it up, and what
the public routines and failure paths do. Apply the new documentation
guidance to the script, test comments and usage documentation.
Executable Python statements are unchanged. Ten focused login checks pass.
* Remove Jenkins login pytests
Remove the provisional test file from the Jenkins login change at the
user’s request. Keep the login script and workflow guidance unchanged.
* Document Jenkins access and test authoring
Add a Jenkins README and a separate authoring skill for simple,
reproducible pipelines and coordinated live-job changes. Keep API access
in its existing skill and route both workflows from AGENTS.md.
Place the login script with the Jenkins files and update its references.
Runtime statements and the credential location are unchanged. Login help,
import, live HTTPS identity, skill validation and local links pass.
* Prefer relevant Jenkins evidence in test reports
Add shared guidance for choosing checks and explaining what their results
establish. Lead PR reports with relevant Jenkins build links, include local
checks when they add evidence, and keep unexpected failures visible.
Connect validation and change-message workflows to the shared skill.
Skill metadata and local guidance links validate; only Markdown changes.
* Keep README verification notes in change reports
Remove the authoring-history sentence from the Jenkins README and clarify
where the README skill should record example verification. Review the PR
documentation for similar notes while retaining reader-relevant setup.
Skill metadata, local links and diff formatting checks pass.
* Group related skills under their entry points
Nest documentation guides and Jenkins test authoring while preserving
skill names and workflow text. Rebase links, make shared parent guidance
explicit, and use recursive skill discovery for validation.
The Codex skill loader discovers every nested child. Recursive schema,
link and preservation checks pass.
* Clarify Jenkins test authoring scope and when to wait
Require a user request before changing Jenkins test definitions, while allowing
relevant existing branch builds during normal validation. Align pytest
integration guidance with that boundary.
Guide intermediate work toward fast meaningful checks and later review of
slow builds; weigh longer waits at final validation and report pending results.
All 20 skill schemas and 99 local guidance links validate; diff formatting
passes. No pipeline or runtime changes, or live Jenkins actions.
* Explain Jenkins permissions before promising site changes
Describe the permissions needed to read, run, create or edit jobs without
assuming a particular account. Link the guidance from authoring and setup,
and explain how to use assigned tokens or switch saved accounts.
All 20 skill schemas and 101 local guidance links pass, including the new
section anchors. Diff formatting passes; this commit changes Markdown only.
Prior live HTTPS checks confirmed creation, build and cancellation access,
read-only configuration access, and denied configuration writes.
* Add branch finalization workflow and agent PR conventions
Define merge preparation as a full branch audit followed by current validation
and a commit, push and draft-PR handoff. Pause for substantive unintended
issues the user has not accepted; allow minor cleanup without interruption.
Route finalization from AGENTS and shared testing guidance. Keep agent PRs
as drafts and sign PR comments posted through a user account with the agent name.
Codex discovers all 21 repo skills. All 21 schemas and 110 local guidance
links validate; diff formatting passes. Only agent guidance changes.
* Clarify which builds an agent may cancel
Limit cancellation to builds and queue items launched for the current task
unless the user authorizes stopping others. A shared Jenkins username does
not establish ownership. Wrap the nearby setup and authoring text.
Final branch audit found no substantive blockers. Login smoke checks passed
for live HTTPS authentication, private credential replacement and failure
preservation without changing the user credential file. All 21 skill schemas,
110 local links and 5 heading anchors pass; Codex discovers all 21 skills.
2026-10-16 20:13:25 -0500eb23a4c1b51706cad0060c28d8c5ead8da595e1cAdd Jenkins workflows and branch finalization guidance (#1396)delete.agents/skills/clubb-change-messages/SKILL.mdedit.agents/skills/clubb-documentation/SKILL.mdedit.agents/skills/clubb-jax-port/SKILL.mddelete.agents/skills/clubb-file-descriptions/SKILL.mdadd.agents/skills/clubb-documentation/readmes/SKILL.mdedit.agents/skills/clubb-pytests/SKILL.mdadd.agents/skills/clubb-finalization/SKILL.mdadd.agents/skills/clubb-documentation/language/SKILL.mdedit.agents/skills/clubb-numerical-diagnosis/SKILL.mddelete.agents/skills/clubb-readmes/SKILL.mdadd.agents/skills/clubb-testing-and-reporting/SKILL.mdadd.agents/skills/clubb-documentation/file-descriptions/SKILL.mdaddjenkins_tests/README.mdaddjenkins_tests/jenkins_api_login.pyedit.agents/skills/clubb-host-compatibility/SKILL.mdadd.agents/skills/clubb-documentation/code-comments/SKILL.mddelete.agents/skills/clubb-doc-language/SKILL.mdedit.agents/skills/clubb-python-api/SKILL.mdadd.agents/skills/clubb-documentation/change-messages/SKILL.mdadd.agents/skills/clubb-jenkins/test-authoring/SKILL.mdedit.agents/skills/clubb-script-cli/SKILL.mdedit.agents/skills/clubb-fortran-port/SKILL.mddelete.agents/skills/clubb-code-comments/SKILL.mdedit.agents/skills/clubb-jenkins/SKILL.mdedit.agents/skills/clubb-column-refactor/SKILL.mdeditAGENTS.md
- src/Microphys/microphys_init_cleanup.F90d9e8b9588ff7b16679ca79b67fcf5382bcc723c41792209029000http://carson.math.uwm.edu/jenkins/user/noreplynoreplynoreply@github.comReset microphysics defaults when initializing another case (#1398)
Restore module and saved-local namelist defaults before reading a new case.
This prevents omitted settings from inheriting the previous case's values. This isn't an issue for any way that clubb is currently run in the codebase, but would potentially cause an issue for a future use case (this is foreshadowing).
2026-10-16 22:50:29 -0500d9e8b9588ff7b16679ca79b67fcf5382bcc723c4Reset microphysics defaults when initializing another case (#1398)editsrc/Microphys/microphys_init_cleanup.F90
- clubb_jax/src/CLUBB_core/sfc_varnce_module.pyclubb_jax/src/CLUBB_core/new_hybrid_pdf_main.pyclubb_jax/src/CLUBB_core/model_flags.pyclubb_jax/src/CLUBB_core/adg1_adg2_3d_luhar_pdf.pyclubb_jax/src/CLUBB_core/interpolation.pyclubb_jax/src/CLUBB_core/parameters_tunable.pyclubb_jax/src/CLUBB_core/precipitation_fraction.pyclubb_jax/src/CLUBB_core/advance_wp2_wp3_module.pyclubb_jax/src/CLUBB_core/setup_clubb_pdf_params.pyclubb_jax/src/CLUBB_core/advance_windm_edsclrm_module.pyclubb_jax/src/CLUBB_core/jax_stats.pyclubb_jax/src/CLUBB_core/file_functions.pyclubb_jax/src/CLUBB_core/grid_class.pyclubb_jax/src/CLUBB_core/advance_clubb_core_module.pyclubb_jax/src/CLUBB_core/advance_xm_wpxp_module.pyclubb_jax/src/CLUBB_core/advance_xp2_xpyp_module.pyclubb_jax/src/CLUBB_core/mono_flux_limiter.pyclubb_jax/src/CLUBB_core/fill_holes.pyclubb_jax/src/CLUBB_core/stats_netcdf.pyclubb_jax/src/CLUBB_core/clip_explicit.pyclubb_jax/src/CLUBB_core/mixing_length.pyclubb_jax/src/CLUBB_core/err_info.pyclubb_jax/pytests/auto_llm_generated_pytests/test_sfc_varnce_diagnostics.pyclubb_jax/src/CLUBB_core/pdf_params.pyclubb_jax/pytests/auto_llm_generated_pytests/test_core_diagnostics.pyclubb_jax/src/CLUBB_core/remapping_module.pyclubb_jax/src/CLUBB_core/sponge_layer_damping.pyclubb_jax/src/CLUBB_core/new_pdf.pyclubb_jax/src/CLUBB_core/matrix_operations.pyclubb_jax/src/CLUBB_core/pdf_closure_module.pyclubb_jax/src/CLUBB_core/pos_definite_module.pyclubb_jax/src/CLUBB_core/numerical_check.pyclubb_jax/src/CLUBB_core/matrix_solver_wrapper.pyclubb_jax/src/CLUBB_core/corr_varnce_module.pyclubb_jax/src/CLUBB_core/new_tsdadg_pdf.pyc47faf30cea562966e64eedc259a5074c6cf89b11792221315000http://carson.math.uwm.edu/jenkins/user/noreplynoreplynoreply@github.comRestore missing debug printouts in JAX core (#1390)
* Restore missing debug printouts in JAX core
The port kept many failure checks but omitted their Fortran messages, making
failed columns and solvers difficult to diagnose. Restore runtime messages,
column headers and available field dumps with the source debug gates. Record
diagnostics needing unported machinery in the skip report.
BFB is not established by the available comparisons. All 23 curated CPU
JAX/Fortran cases matched within default tolerances: absolute 1e-7 and
percentage 1e-7%, or 0.001% for the curated Morrison cases. Runs used four
columns, standard statistics and existing durations/caps. Separately, 24
starting-tree kernel comparisons found exactly equal result/state values.
The CPU JAX suite passed 787 tests, including compiled diagnostic checks;
the focused rerun passed 14. Source/diff review and git diff --check passed.
* Remove diagnostic restoration report
Remove the standalone report on intentionally skipped diagnostics. Observed
Fortran differences remain documented in the affected JAX modules.
This removes documentation only, so model/output BFB is not applicable.
Diff review, a tracked-file reference search and git diff --check passed.
Runtime tests were not rerun for this deletion.
* Identify scalar fields in solver diagnostics
The separate scalar solves all printed the same generic field label. Restore
the Fortran names sclrp2, sclrprtp and sclrpthlp so a failure identifies which
variance or covariance solve failed.
Source comparison confirms the three labels match their Fortran call sites.
Python syntax and whitespace checks passed. Jenkins validation will exercise
the published revision.
2026-10-17 02:15:15 -0500c47faf30cea562966e64eedc259a5074c6cf89b1Restore missing debug printouts in JAX core (#1390)editclubb_jax/src/CLUBB_core/pdf_closure_module.pyeditclubb_jax/src/CLUBB_core/pdf_params.pyeditclubb_jax/src/CLUBB_core/new_hybrid_pdf_main.pyeditclubb_jax/src/CLUBB_core/grid_class.pyeditclubb_jax/src/CLUBB_core/interpolation.pyeditclubb_jax/src/CLUBB_core/advance_xp2_xpyp_module.pyeditclubb_jax/src/CLUBB_core/adg1_adg2_3d_luhar_pdf.pyeditclubb_jax/src/CLUBB_core/numerical_check.pyeditclubb_jax/src/CLUBB_core/err_info.pyeditclubb_jax/src/CLUBB_core/new_pdf.pyaddclubb_jax/pytests/auto_llm_generated_pytests/test_sfc_varnce_diagnostics.pyeditclubb_jax/src/CLUBB_core/advance_windm_edsclrm_module.pyeditclubb_jax/src/CLUBB_core/setup_clubb_pdf_params.pyeditclubb_jax/src/CLUBB_core/corr_varnce_module.pyeditclubb_jax/src/CLUBB_core/advance_xm_wpxp_module.pyeditclubb_jax/src/CLUBB_core/new_tsdadg_pdf.pyeditclubb_jax/src/CLUBB_core/model_flags.pyeditclubb_jax/src/CLUBB_core/mono_flux_limiter.pyeditclubb_jax/src/CLUBB_core/pos_definite_module.pyeditclubb_jax/src/CLUBB_core/matrix_operations.pyeditclubb_jax/src/CLUBB_core/jax_stats.pyeditclubb_jax/src/CLUBB_core/clip_explicit.pyeditclubb_jax/src/CLUBB_core/fill_holes.pyeditclubb_jax/src/CLUBB_core/sponge_layer_damping.pyeditclubb_jax/src/CLUBB_core/remapping_module.pyeditclubb_jax/src/CLUBB_core/matrix_solver_wrapper.pyeditclubb_jax/src/CLUBB_core/mixing_length.pyeditclubb_jax/src/CLUBB_core/parameters_tunable.pyeditclubb_jax/src/CLUBB_core/precipitation_fraction.pyeditclubb_jax/src/CLUBB_core/advance_wp2_wp3_module.pyaddclubb_jax/pytests/auto_llm_generated_pytests/test_core_diagnostics.pyeditclubb_jax/src/CLUBB_core/file_functions.pyeditclubb_jax/src/CLUBB_core/advance_clubb_core_module.pyeditclubb_jax/src/CLUBB_core/stats_netcdf.pyeditclubb_jax/src/CLUBB_core/sfc_varnce_module.py
githttp://carson.math.uwm.edu/jenkins/user/noreplynoreplynoreplyfalseStarted by an SCM change000076075751060.9919682968259609499c45d0ef25810f48bbd43c8f92afa1497caa09499c45d0ef25810f48bbd43c8f92afa1497caarefs/remotes/origin/master09499c45d0ef25810f48bbd43c8f92afa1497caa09499c45d0ef25810f48bbd43c8f92afa1497caarefs/remotes/origin/master09499c45d0ef25810f48bbd43c8f92afa1497caa09499c45d0ef25810f48bbd43c8f92afa1497caarefs/remotes/origin/masterhttps://github.com/larson-group/clubb.gitfalse#5967607593290clubb_BFB_r8029_flags_gfortran_test #596596false59610653SUCCESS1792139230965http://carson.math.uwm.edu/jenkins/job/clubb_BFB_r8029_flags_gfortran_test/596/- .agents/skills/clubb-column-refactor/SKILL.mdclubb_jax/AGENTS.md.agents/skills/clubb-jenkins/SKILL.mdtests/README.mdLLM_prompts/port_underlying_fortran_to_other_languages.mdLLM_prompts/README.md.agents/skills/clubb-session-retrospective/references/guidance_maintenance.mdtuner/pytests/auto_llm_generated_pytests/README.md.agents/skills/clubb-script-cli/SKILL.mdtests/pytests/auto_llm_generated_pytests/README.mdLLM_prompts/SHORTCUTS.mdLLM_prompts/update_host_models_after_clubb_changes.mdLLM_prompts/pytest_workflow.mdclubb_jax/JAX_CONVERSION_PLAN.mdLLM_prompts/fortran_routine_formatting.md.agents/skills/clubb-fortran-port/SKILL.md.agents/skills/clubb-python-api/SKILL.md.agents/skills/clubb-dash/SKILL.mdLLM_prompts/script_cli_conventions.mdutilities/pytests/auto_llm_generated_pytests/README.md.agents/skills/clubb-numerical-diagnosis/SKILL.mdLLM_prompts/update_python_api_and_drivers.md.agents/skills/clubb-session-retrospective/SKILL.mddash_app/pytests/auto_llm_generated_pytests/README.mdLLM_prompts/jenkins_workflow.mdLLM_prompts/change_messages.mdLLM_prompts/dash_app_workflow.md.agents/skills/clubb-jax-port/SKILL.mdLLM_prompts/numerical_regression_workflow.md.agents/skills/clubb-host-compatibility/SKILL.md.agents/skills/clubb-fortran-format/SKILL.mdAGENTS.md.agents/skills/clubb-pytests/SKILL.mdLLM_prompts/session_retrospective.mdLLM_prompts/fortran_column_refactor.md.agents/skills/clubb-change-messages/SKILL.mdLLM_prompts/jax_porting_workflow.md09499c45d0ef25810f48bbd43c8f92afa1497caa1792123599000http://carson.math.uwm.edu/jenkins/user/noreplynoreplynoreply@github.comConsolidate CLUBB workflows into skills (#1394)
* Consolidate CLUBB workflows into skills
Move the 13 workflows into repo skills and route to them from AGENTS.md,
removing the legacy shortcut index and prompt directory. Keep the existing
five skill identities and workflow instructions, including the scope rules
previously stored in the index. Update only paths and obsolete routing text.
Preservation checks passed for all workflow bodies, existing skill metadata,
scope rules and task selectors. All 13 skills validate, all 55 local links
resolve, and git diff --check passed. BFB is not applicable to this
documentation-only migration.
* Clarify skill selection and local guidance
Allow multiple relevant skills in the task instructions, name user-facing
documentation clearly, and explain that the ignored worklog is local to
each checkout and should be created when absent. Add verified private
host-repository links near the top of the compatibility skill so readers
can identify the models and their access requirements.
BFB is not applicable to these documentation-only clarifications. All 13
skill schemas, local guidance links, and git diff --check pass. Existing
host workflow instructions are preserved.
2026-10-15 23:06:39 -050009499c45d0ef25810f48bbd43c8f92afa1497caaConsolidate CLUBB workflows into skills (#1394)deleteLLM_prompts/change_messages.mddeleteLLM_prompts/fortran_column_refactor.mdedit.agents/skills/clubb-session-retrospective/SKILL.mddeleteLLM_prompts/script_cli_conventions.mdedittests/pytests/auto_llm_generated_pytests/README.mddeleteLLM_prompts/update_host_models_after_clubb_changes.mdeditdash_app/pytests/auto_llm_generated_pytests/README.mddeleteLLM_prompts/pytest_workflow.mdadd.agents/skills/clubb-column-refactor/SKILL.mdadd.agents/skills/clubb-jenkins/SKILL.mdadd.agents/skills/clubb-python-api/SKILL.mdedit.agents/skills/clubb-script-cli/SKILL.mdedit.agents/skills/clubb-jax-port/SKILL.mdadd.agents/skills/clubb-session-retrospective/references/guidance_maintenance.mddeleteLLM_prompts/SHORTCUTS.mdadd.agents/skills/clubb-dash/SKILL.mdeditAGENTS.mdeditclubb_jax/AGENTS.mdeditutilities/pytests/auto_llm_generated_pytests/README.mdedit.agents/skills/clubb-change-messages/SKILL.mddeleteLLM_prompts/fortran_routine_formatting.mddeleteLLM_prompts/dash_app_workflow.mdeditclubb_jax/JAX_CONVERSION_PLAN.mdadd.agents/skills/clubb-host-compatibility/SKILL.mdedittests/README.mddeleteLLM_prompts/update_python_api_and_drivers.mddeleteLLM_prompts/numerical_regression_workflow.mdedit.agents/skills/clubb-pytests/SKILL.mddeleteLLM_prompts/jenkins_workflow.mdedittuner/pytests/auto_llm_generated_pytests/README.mdadd.agents/skills/clubb-fortran-port/SKILL.mddeleteLLM_prompts/jax_porting_workflow.mddeleteLLM_prompts/port_underlying_fortran_to_other_languages.mddeleteLLM_prompts/README.mddeleteLLM_prompts/session_retrospective.mdadd.agents/skills/clubb-fortran-format/SKILL.mdadd.agents/skills/clubb-numerical-diagnosis/SKILL.md
githttp://carson.math.uwm.edu/jenkins/user/noreplynoreplyfalse597http://carson.math.uwm.edu/jenkins/job/clubb_BFB_r8029_flags_gfortran_test/597/595http://carson.math.uwm.edu/jenkins/job/clubb_BFB_r8029_flags_gfortran_test/595/